Biology subjects

Cheng, M. T. K.

Publications and source records attributed to Cheng, M. T. K..

3 recordsLinked to original sources

bioRxiv2026

Mitigation of imprinted antibody responses in elderly COVID-19 highly vaccinated individuals

SARS-CoV-2 continues to evolve from the Omicron serotype, with BA.2.86 sublineage JN.1 and descendants predominating in 2025-26 and recent emergence of the highly divergent BA.3.2 saltation variant. Elderly individuals continue to be at greatest risk of clinical complications from COVID-19, yet contemporary data on kinetics of immune potency and breadth following multiple vaccinations remain limited in this group. We studied a cohort of forty-three healthy older adults (median age = 85 years, IQR 75-88, 40% female). Using both pseudotyped virus (PVNT) and surrogate virus (SVNT) neutralization-based assays, we demonstrate that JN.1 and KP.2 vaccinations six months apart elicit high potency neutralization across all studied variants except BA.3.2.2, where titres were around 2-3 fold lower. Waning of serum neutralizing activity was modest between vaccine doses, suggesting sustained immunity following multiple vaccines. Importantly, the half-life of serum neutralization against Wu-1 (179 days) was substantially longer compared to JN.1 subvariants (43.7-70.1days), consistent with imprinted and longer-lived Wu-1-specific responses. Furthermore, half-life for BA.3.2.2 neutralisation was prolonged at 107 days compared to JN.1 subvariants, implicating imprinted ancestral variant targeting antibodies in neutralization of this saltation variant. While absolute neutralization titers remained highest against ancestral Wu-1 at all timepoints due to multiple historical exposures and accumulation, the recall responses after the recent KP.2 vaccine revealed a shift in immunodominance: neutralization against full-length Wu-1 spike was not boosted, whereas all tested JN.1 descendants and BA.3.2.2 showed significant boosts, indicating that immune imprinting against ancestral Wu-1 was partially overcome. These data indicate that in the elderly, protective neutralizing antibody responses against recent VOC can be achieved, with alleviation of immune imprinting and reduction of waned responses through biannual, strain-updated booster vaccines. Imprinted antibodies against ancestral pre Omicron variants may still be relevant for protection against further highly immune evasive variants such as BA.3.2.2, highlighting that careful characterisation of population level COVID-19 humoral immunity is still warranted.

microbiology↗

bioRxiv2024

Nasopharyngeal specific selection and emergence of SARS-CoV-2 spike fusion peptide mutation P812S during chronic infection

Omicron emergence represented a seismic event in the COVID-19 pandemic, demonstrating what was essentially antigenic shift in a virus that cannot reassort its genome as influenza can. Understanding the success of Omicron is essential, and yet we have little understanding of the biological underpinnings of its ability to accommodate diverse mutations and bring together deleterious mutations to generate a highly successful new serotype. Persistent SARS-CoV-2 infections are a likely source of new variants and may provide valuable insight into past and future evolutionary trajectories, in particular those involving allosteric interactions that defy genotype to phenotype prediction. Here we observe upper airway specific evolution of SARS-CoV-2 demonstrating fusion peptide (FP) domain mutation S:P812S adjacent to the S2 cleavage site that emerged during a chronic infection in an immunocompromised individual. Indeed, this mutation had previously emerged in an ancestral B lineage as well as the delta variant lineage and transmitted successfully in populations globally, though remains uncharacterised. P812S in spike pseudotyped virus particles did not impact entry efficiency across cell lines expressing endogenous ACE2 and TMPRSS2. However, efficiency of spike cleavage at S1/S2 was reduced and molecular dynamics simulation demonstrated altered S1/S2 loop conformations that possibly impacted furin mediated cleavage. Consistent with impaired S1/S2 cleavage, and reminiscent of Omicron BA.1, cell-cell fusogenicity was severely impaired by introduction of P812S. The mutation also introduced significant perturbations to the FP region and also affected protomer-protomer packing. P812S conferred evasion of a neutralising monoclonal antibody targeting the fusion peptide, consistent with significant structural rearrangements in the FP region. Finally, P812S bearing viruses showed evasion of polyclonal neutralising antibodies in sera from vaccinated individuals at 32{degrees}C (simulating upper respiratory tract) and to a lesser extent at 37{degrees}C. Thus we report a novel mutational adaptation to the upper airway allowing enhanced immune evasion to fusion peptide targeting neutralising antibodies that also incurs a defect in ability to induce syncytia. These data shed light on the balance between upper airway adaptation/immune evasion by SARS-CoV-2, ability to induce syncytia formation, and disease severity given the established link between syncytia and severe COVID-19.

immunology↗

bioRxiv2023

Contrasting functions of ATP hydrolysis by MDA5 and LGP2 in viral RNA sensing

Cytosolic long double-stranded RNA (dsRNA), among the most potent proinflammatory signals, is recognized by MDA5. MDA5 binds dsRNA cooperatively, forming helical filaments. ATP hydrolysis by MDA5 fulfills a proofreading function by promoting dissociation of shorter endogenous dsRNAs from MDA5 while allowing longer viral dsRNAs to remain bound leading to activation of interferon-{beta} responses. Here, we show that adjacent MDA5 subunits in MDA5-dsRNA filaments hydrolyze ATP cooperatively, inducing cooperative filament disassembly. This amplifies the RNA footprint expansion that accompanies each round of ATP hydrolysis and allows MDA5 to displace tightly bound proteins from dsRNA. Our electron microscopy and biochemical assays show that LGP2 binds to dsRNA at internal binding sites through noncooperative ATP hydrolysis. Unlike MDA5, LGP2 has low nucleic acid selectivity and can hydrolyze GTP and CTP as well as ATP. Binding of LGP2 to dsRNA promotes nucleation of MDA5 filament assembly resulting in shorter filaments. Molecular modeling of the MDA5-LGP2 interface suggests that MDA5 interacts with dsRNA stem-bound rather than end-bound LGP2. We conclude that NTPase-dependent binding of LGP2 to internal sites on dsRNA increases the number and signaling output of MDA5-dsRNA complexes. Our work identifies novel molecular mechanisms contributing the selectivity and sensitivity of cytosolic dsRNA sensing. KEY POINTSO_LICooperative ATP hydrolysis in MDA5 filaments confers selectivity for dsRNA and displaces other proteins from RNA C_LIO_LINoncooperative NTP hydrolysis by LGP2 induces binding to internal RNA sites with low selectivity C_LIO_LIRNA stem-bound LGP2 nucleates assembly of MDA5 signaling complexes on a broader set of RNA ligands C_LI

biochemistry↗